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SIS Converter

Universal Converter for the Most Common Scientific Imaging File Formats

Using SIS Converter

Opening the arivis SIS Converter

  1. Execute arivis SIS Converter by clicking on the related icon on the desktop.
  2. The arivis SIS Converter dialog opens.

Complex Import

To import complex, unknown, image structures, select the Custom Import scenario.

It enables you to freely define your import scenario in detail. If the suggested scenarios do not fit your need, this dialog is your partner in defining your import scenario.

Manual import mapper

The Manual import mapper displays a table with information about what regions of the input files are mapped to what regions in the destination file. Initially, each channel of the input data is specifically mapped to the destination file and will be presented as one line in the mapping table.

For a large number of files, the Manual Mapper approach is not suitable.

The Selection menu provides you with easy-to-use wizards to perform different tasks in order to create custom mappings. Before accessing a specific wizard, please mark all lines inside the mapping table that you want to change. You can press CTRL-A to mark all input files at once.

Apply dimension order

By applying dimension templates to your input files, you can easily define how your images are arranged in the different dimensions which the internal image model provides. If you have, for example, input files for two channels that should be organized as a result dataset with 10 time points and 20 planes, you can configure the dimension order as shown in the following screenshot:

Pattern matching

Sometimes the filenames contain information that define on which dimension each image has to be located in the resulting image.

  1. Choose Selection > Pattern matching... to open the import pattern matching dialog. Here you can define a pattern that contains specific identifiers that mark parts of the input filename as a locator for an image dimension.
  2. The identifiers match numeric values (including leading zeros). Use the wildcard identifiers * and ? to ignore other numeric values. If your input files start counting a dimension at 100, Edit offsets helps you set a new start for counting. E.g. if your first input file is named "input_plane0100_frame010_channel01", and you don't adjust the offsets, your resulting file may contain empty data. To alleviate this change the plane offset to -100, the time point offset to -10, and the channel offset to -1. Now your resulting file will only contain the data you set up to import.
  3. Press the Refresh button to refresh the preview of how the current pattern affects your import scenario in the lower preview panel.

Detecting channel names

Sometimes the filenames contain information about channel names.

  1. Choose Selection > Detect Channel Names... to open the Detect Channel Names dialog box. Here you can define a pattern that matches a channel name and map it to a resulting channel.
    You can use this mechanism to import multiple input files with a single channel into a single file with multiple channels.
  2. If your import data contains more than one channel use Add to create another channel for your import result.
  3. Use Update preview to check, if your channel patterns match with your import data.

Saving import scenario definitions

  1. To store your import scenario definition, you need to open the Custom import dialog box by pressing More options... and Perform custom import....
  2. After checking that the mapping table reflects your import scenario, choose File > Save import scenario... in order to save this import scenario to a file on your computer.

Supported image formats

arivis SIS Converter supports a large number of image formats. Media handlers are extension plug-ins which enable arivis SIS Converter to import and export files in various file formats. For instance, the importers and exporters use these media handlers.

The following media-handlers are available in your arivis SIS Converter:

Amira-Mesh Media Handler

The Amira-Mesh media handler enables the import of Amira-Mesh files, containing uniform lattice data. Amira-Mesh files can contain different types of data, for instance spatial graphs or stacked lattices. This media handler is not able to read these special data types.

The Amira-Mesh media handler allows you to import images of the following file format: Amira-Mesh (*.am)

Aperio Media Handler

The Aperio media handler allows you to import images of the following file format: Aperio (JPEG) (*.svs) , Aperio JPEG2000) (*.svs)

Metamorph Media Handler

The Metamorph media handler is part of the Bio Media Handler Module which enables the import of some common image formats used in biology-related working areas.

The Metamorph media handler allows you to import images of the following file format: Metamorph (*.stk)

The DeltaVision media handler

The DeltaVision media handler enables the import of Applied Precision's DeltaVision image files.

The DeltaVision media handler allows you to import images of the following file format: DeltaVision (*.dv)

Dicom Media Handler

The Dicom media handler enables arivis SIS Converter to read DICOM containers or DICOMDIR files. These files describe the structure of a DICOM dataset (Digital Imaging and Communications in Medicine) that is most commonly used in medical working areas.

The Dicom media handler allows you to import images in the following file formats: Dicom (*.dcm) , DICOMDIR (*.dicomdir)

Hamamatsu Media Handler

The Hamamatsu media handler allows you to import images of the following file format: NDPI (*.ndpi) , Virtual Microscope Specimen (*.vms)

ICS Media Handler

The ICS media handler allows you to import images of the following file format: ICS 1.0 (*.ics) , ICS 2.0 (*.ids)

JPEG Media Handler

The JPEG media handler enables an optimized import of JPEG image files.

It allows you to import images of the following file format: JPEG (*.jpg, *.jpeg)

Leica Media Handler

The Leica media handler enables the import of Leica image file formats.

The Leica media handler allows you to import images of the following file formats: Leica Image File Format (*.lif) , Leica LCS (*.lei)

LSM Media Handler

The LSM media handler enables the import of the LSM file formats.

Mirax Media Handler

The Mirax media handler enables the import of the Mirax SlideAC file format. This image format originates from Carl Zeiss Mirax Slide scanner systems and is based on image pyramids.

The Mirax media handler allows you to import images of the following file format: Mirax SlideAC (*.mrxs)

NIfTI Media Handler

The NIfTI media handler enables the import of the NIfTI (Neuroimaging Informatics Technology Initiative) image file formats.

The NIfTI media handler allows you to import images of the following file formats: single-file(combined data and meta- data)(.nii) ,single-file gzip-compressed (.nii.gz) , dual- file(separate data and meta-data, respectively)(.img/.hdr)

Nikon Media Handler

The Nikon media handler enables the import of data created by the Nikon imaging solutions.

The Nikon media handler allows you to import images of the following file format: Nikon ND2 (*.nd2)

Olympus Media Handler

The Olympus media handler enables the import of the Olympus OIB/OIF file formats.

The Olympus media handler allows you to import images of the following file formats: Olympus OIB (*.oib) , Olympus OIF (*.oif)

RAWInfo Media Handler

The RAWInfo media handler enables the import of raw image files by using a control (*.rawinfo) file that contains dimension information.

The Raw media handler allows you to import images of the following file formats: RawInfo (*.rawinfo)

Slide Book Media Handler

The Slide Book media handler enables the import of the Slide Book file format.

The Slide Book media handler allows you to import images in the following file format: Slide Book (*.sld)

Tiff Media Handler

The Tiff media handler enables the import of TIFF (Tagged Image File Format) based image file formats. TIFF is a commonly used format to store images.

The Tiff media handler allows you to import images of the following file formats: TIFF (*.tif, *.tiff) , OME TIFF (*.tif, *.tiff)

VOL Media Handler

The VOL media handler enables the import of VG Studio VOL images.

The VOL media handler allows you to import images of the following file format: VOL (*.vol/*.vgi)

To import a VG Studio VOL dataset both files (.vol & .vgi) are needed!

Release Notes

SIS Converter (Pro) 4.1 Release

Announcing the latest release of the arivis SIS Converter and arivis SIS Converter Pro

Bugfixes

  • Pixel size for multiple image sets using custom import
  • CZI import with different pixel types (in one data set)
  • Possible problem with Nikon ND2 import for pre-stitched data
  • Avoid conversion history corruption
  • Small UI glitches
  • Separate Start Menu entries for the free and the pro version
  • Avoid infinite loop with the same source and destination folders (SIS Converter PRO)
  • Improved robustness for unexpected termination

DOWNLOAD FREE VERSION

 

Supported File Formats

Supported Image File Formats

SIS Converter and Converter Pro *as of Dec 2022*

  • Abberior Imspector (.obf, .msr)
  • AmiraMesh (*.am)
  • Aperio SVS (*.svs)
  • arivis Single Image Stack 3 (*.sis)
  • BigDataViewer file format (*.xml)
  • CompuServe GIF (*.gif, *.giff)
  • DeltaVision image file (*.dv)
  • DICOM Directory (*.dicomdir, *.DICOMDIR)
  • DICOM Image (*.dcm)
  • Fiji/ImageJ-TIFF (*.tif, *.tiff)
  • GE InCell (*.xdce)
  • Hamamatsu tiff-like file format (*.ndpi)
  • High Dynamic Range Image (*.hdr)
  • ICS 1.0/2.0 file format (*.ics, *.ibs)
  • Imaris IMS (*.ims)
  • Imspector (*.obf/*.msr)
  • JPEG/JFIF (*.jpg, *.jpeg, *.jif, *.jfif, *.j, *.jpe)
  • JPEG-2000 (*.jp2, *.j2k, *.j2c)
  • Leica Image File Format (*.lei,*.lif)
  • Luxendo images (saved as BigDataViewer *.xml)
  • Metamorph STK (*.stk)
  • Mirax SliceAC file format (*.mrxs)
  • Molecular Devices (GE IN Carta)
  • Neuroimaging Informatics Technology Initiative Image File Format (*.hdr, *.nii, *.nii.gz)
  • Nikon ND2 files (*.nd2)
  • Olympus file format (*.oir, *.oib, *.oif)
  • Olympus Media Handler (*.vsi)
  • OME-TIFF (*.tif, *.tiff)
  • OME-TIFF/FEI (*.tif, *.tiff)
  • OME-TIFF/LaVision (*.tif, *.tiff)
  • Perking Elmer PE (standard PE format, .qptiff  Columbus metadata)
  • Portable Network Graphics (*.png)
  • Slidebook (.sld) Media Handler
  • TIFF Tagged Image (*.tif, *.tim, *.tiff)
  • TillVision file formats (*.rbinf, *.ini)
  • TrakEM2 Image file format (trakem2.xml, *.xml)
  • VGI/VOL Media Handler
  • VG Studio Max (*.vgl)
  • VG Studio Images VOL Media Handler (*.vol, *.vgi)
  • Virtual Microscopy Specimen file format (*.vms, *.vmu)
  • Windows Bitmap (*.bmp, *.rle, *.vga, *.rl4, *.rl8, *.sys)
  • Zeiss Axiovision ZVI (*.zvi)
  • Zeiss CZI/ZISRAW (*.czi, *.zisraw)
  • Zeiss LSM-tiff (*.lsm)
  • Yokogawa CV (*.mlf)
  • Yokogawa CPf (*.mmd)

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